First of all I am not endorsing Intelligent Design (Wikipedia link); I'm asking this because I (someone who does not have a background in biology, organic chemistry, or philosophy) got into a conversation with someone who does endorse it, and I'm trying to see his point of view as far as rationality can allow. Second of all, I apologize for any vagueness; Intelligent Design isn't well enough defined as a theory for me to help that. I also apologize if this is rehashing content already plentiful on the Internet, but for my purposes I can't simply depend on the likes of Wikipedia or Talk Origins, so what I'm looking for here instead is to take the opposite approach and see, based on your informed minds, if there could possibly be any reasonable likelihood of an ideal ID theory being adopted.

I'm looking for the most favorable consideration for what ID might be
if it were best developed as a viable hypothesis or theory to get an
idea of how far such a discussion is worth taking. An unbiased,
informed Devil's advocate, if you will.

My cursory investigation of what Stephen Meyers (video link) and Michael Behe (video link) say (correct me if I'm wrong) seems to be that either the first cell was likely designed intelligently judging by the complex code of DNA and that evolution took course from there, or that the first cells were made and many instances of evolution were from some kind of intelligently guided mutations as was needed to make "irreducibly complex" cells or body functions (whether the guidance stops after the Cambrian or continued even to the point of making different types of new bacteria and different types of apes/humans or whether every single mutation and adaptive ability is being guided, I'm not sure if they're at any consensus, and that's why I don't know if I should stop my question at abiogenesis or include evolution). The person I spoke with also brought up some specific claims (everything looks designed, DNA has ordered, complex information, blood clotting is irreducibly complex, ID can and has make predictions like decades ago that "Junk DNA" wasn't junk) that I don't need you to debunk (I have Google).

But if there could be any possible support or truth to any of the above, I would appreciate knowing about that. (Again, Devil's advocate so I can be informed and understand where the points come from.) Reading an ID book alone, it would be in places hard to know where they differ from actual scientific conclusions. After all, when someone who seems to know what they're talking about and can explain something in technical detail says that something is impossible or extremely unlikely, it's hard for me to know why they would be wrong (are they ignoring other possibilities? misrepresenting facts? are they really right and just getting the cold shoulder from an atheistic scientific community because it implies a deity?). So I focus on mainstream sources, even if they don't bother entertaining ID and leave me ignorant of its possible virtues. And thus I'm hoping someone from this informed community might enlighten me to what those possible virtues might be.

Regarding "junk DNA": The claim of 80% functional DNA is using a very very broad definition of "functional". The claim is strongly debated - for a non-scientific piece see guardian.co.uk/science/2013/feb/24/… . Even if it were true, I do not see how this supports ID.
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BitwiseJul 3 '13 at 1:13

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I'm not certain that this is suitable for a Q&A since you have a large number of questions bundled into one. As it reads now it deals with an entire "theory", and this cannot be explained in a single answer. Would it be possible to narrow down to the aspects that you are most interested in (and you could ask follow-up questions afterwards)?
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fileunderwaterJul 3 '13 at 7:39

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Oh boy. @Bitwise, that’s a pretty bad article, even the title gets it wrong – ENCODE does not claim that junk DNA is “vital to life”. The “80% is functional” claim says nothing about necessity of that function. If ENCODE had made this claim (and if it were correct) then it’s true that the ID proponents in the 60s would have made a correct prediction (albeit for the wrong reasons). As it happens, this claim is a strawman.
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Konrad RudolphJul 3 '13 at 10:16

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If you look at any actual biological systems, its pretty clear they are too complicated to have been designed! Who would design a system with so much waste, multiple receptors and multiple ligands in each system, only a handful of which seem to actually do anything. The more you look at biology, the more absurd the idea it was designed!
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NickJul 3 '13 at 10:58

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@Nick that just disproves the idea of intelligent design :).
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terdonJul 3 '13 at 15:06

4 Answers
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I think the issue with Intelligent Design is not so much that its patently proven wrong. On the contrary, the problem is that it not a scientific hypothesis and so it really isn't a scientific question.

If I may, the basis of the scientific method, as formulated by Karl Popper, but commonly in use today, is that science is the putting forth of theories of cause and effect which are testable (or if we are being precise, falsifiable).

That is to say, you put forth a theory such as 'God/some diety figure made all living things' and then you perform an experiment which can differentiate whether the hypothesis or its null version (i.e. 'no intelligence is the source of life / biology is the result of accidents') is more likely true.

This question will not be testable in a way to answer enough of the reasonable skeptical questions ( or at least so far it has not). Experiments have been tried, but they are often not acceptable to everyone. For instance the idea that some biological structures such as the eye or the flagellar motor are too complex to have evolved through a typical Darwinian process which involves a series of small changes are almost biological theology - one can always hypothesize a more inhuman God (probably appropriate) who acts and 'thinks' in such an inhuman manner that anything you see could be created/inspired. While I think you should feel free to believe either way, I also believe that this is not an argument that can be won or lost. The tendency for any experiment to confirm both the hypothesis and its inverse seem inescapable.

That is to say, that biology and physics will ultimately fail where philosophy and logic also did in proving the existence of God, besides the less interesting truism that if God does exist, the deity is consistently elusive to proof.

On the other side of the coin, the proof that life has emerged from naturally occurring phenomena such as lighting strikes in a prebiotic environment are interesting since it shows that nucleotides and amino acids might have been available without metabolic pathways to synthesize them. In its way, the molecular origins of life on earth is a question which is really testable only in theory.

Anyone who thinks they are going to re-create the event of the beginning of life itself is scientifically on thin ice - the prebiotic environment may have extended to the entire surface and atmosphere of the earth as well as down into mud and bodies of water and sat incubating for maybe hundreds of millions of years. The idea that the fundamental moment of life generation is just going to show up on a well chosen set of conditions in a 500 ml flasks with some electrodes attached is an idea that workers in the field don't even entertain.

Until such an experiment produces life, the work will have to rely upon the idea that there was a moment in time where the necessary elements came together.

This being said, cosmology, biogenesis work has approached the moment of the genesis of life asymptotically with amazing clarity.

The RNAWorld hypothesis strongly supports the idea that an early biotic system might have been very simple - maybe only RNA and its four nucleotides. Clearly after what Dawkins calls a replicator exists, then the pathway to living things as we know them is pretty easy to envision.

I should add that I'm not one of those people who think that science is everything - the trend that is impoverishing some humanities program is alarming to me. Its just that some things are not science.

I totally agree on testability. Another way to put it: ID makes no predictions, so it's useless - besides being untestable, ergo unscientific.
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Sklivvz♦Jul 5 '13 at 2:40

thanks - Its a common problem even with scientists really - I know I never got this stuff in a class. It also comes up in general with 'new' theories of evolution, relativity, and cosmology - the new theory tries to just make the same prediction as the textbook examples, but doesn't bother to look at the sometimes thousands of other experiments which confirm the established theory but might not confirm theirs.
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shigetaJul 5 '13 at 4:00

The problem with Intelligent Design is that it doesn't appreciate that the forces that shape species (and individual organism) have to be constant and ongoing or the species disappears. The past matters little, it's what happens right here, right now that keeps species in any particular form.

Biological system are not static structures like a building. You put energy into a building when you move and shape it material during construction. Immediately though, the energy in the structure begins to flow out into the ambient environment, causing the building to loose it's structure and decay. Eventually it will fall to dust.

Biological systems are dynamic, not static. A living organism is like a whirlpool. A whirlpool is a complex ordered structure that dissipates energy caused by friction between streams moving at different velocities next to each other. It is never composed of the same molecules of water from moment to moment and once water has passed through the whirlpool it never returns. The whirlpool is the structure, not the transitory water.

Changing the rate of flow, depth of the water, temperature etc changes the exact structure of the whirlpool instantly.

Biological systems are non-material structures like whirlpools. Matter and energy constantly flows into and out of bodies. We stop stop breathing, we die. Your body, even scars and bones are continuously begin torn down and regenerated. The average half life of atoms in your body is seven years. Even atoms that do remain in the body are moved from molecule to molecule and from tissue to tissue. Only the pattern remains semi-constant. Species and individuals organisms are the structures, not the transitory matter.

Changing the flow of matter and energy into an organism, changes it's structure instantly. Changing the flow over long periods, changes entire species.

If I show a picture of a whirlpool in water but crop it so you can't see whether it's occurring in a natural stream or a flow tank in a lab, how could tell whether the whirlpool was artificial or not? You couldn't, because there is no structural difference between an artificial whirlpool and natural whirlpool. They look the same because the same forces and laws create them and do so continuously

The same is true of life.

You can't look at living things and determine whether they are natural or artificial because just like a whirlpool, it is the flow of matter and energy through life, at any particular moment, that defines it's structure.

Even if some intelligence, divine or material, did alter or even start life, it would have to fit into the material environment exactly like one that arose naturally. It would be indistinguishable from a natural one because the same forces would give it shape and maintain it.

So the best argument against intelligent design is that we don't need to evoke it explain how life exist now, moment to moment. If natural forces continuously create and maintain life continuously today, then they had to be able to do so yesterday and the day before, all the back.

ID addresses an obvious question which nearly everyone considers very strongly at some time. Those who don't choose to believe in God will often argue that it is a non-issue. But is it a non-issue because they are so obviously right that others have no right to voice their opinion, or because it doesn't matter? The former is a very childish view, and certainly isn't very helpful if the goal is to convince others of the "correct" view. And if it simply doesn't matter to Atheists, then surely we can all recognize that it matters quite a lot to others. I'm not suggesting that theists simply be allowed to rewrite the curriculum (which some have attempted), but this is a question which costs more time and energy to ignore than to address. And we have a lot to learn from each other in the process.

Many people, as they study evolution, very naturally begin to conclude that life could have, and therefore must have, emerged entirely by accident. This is not so different from observing that autism diagnosis has been on the rise since about the same time a certain vaccine came into widespread use, and the fact that symptoms often set in shortly after said vaccine has been given, and concluding that increased cases of autism could have been, and therefore must have been, caused by the vaccine. There is an appearance of a causal relationship, but the conclusion does not exactly follow from the evidence. In the case of the vaccine suspicions, I'm grateful that they have been solidly proved false now.

As for the true origin of life, many of us think we know the answer. Be that as it may be, this answer is not delivered to us through the study of evolutionary biology. Anyone who tells you that science has proved that we did in fact evolve without any external manipulation into what we are today, or that life emerged completely by chance, is misinterpreting the facts (or more likely, believing a rumor they heard). Anyone who tells you that science has proved the opposite, that life could not have emerged by chance, is likewise not following the logic correctly (or more likely, favors different rumors). I think that it would be a healthy exercise of critical thinking to open up this kind of discussion in a high school biology classroom, consistently reinforcing the fact that none of it on either side of the argument offers any conclusive evidence on the actual true origin of life. People who feel passionately either way on this must cringe a little at this suggestion, perhaps comparing it to the way Fox News feigns a "fair and balanced" presentation by presenting the plain and obvious truth on equal footing with an extremist view. But which is the extremist view on this issue? It depends on where you stand.

The biggest problem I foresee is that most of the instructors are so strongly biased one way or another, that they would have a hard time honestly mediating such a discussion. But, frankly, this is already the case, so I would argue that it is better to formalize this as a critical thinking exercise in the curriculum. It probably won't open anyone to new thinking on the origins of life, but hopefully, it will help them resist the next vaccine scare. And it will help them to distinguish scientific proof from speculation or belief. For many religious students, this will allow them to digest the rest of the material without feeling like it is an attack on their sacred beliefs.

If anyone down-votes for actual problems with the quality of my answer to the specific question that was asked, please educate me on my failure with a comment.
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Mark BaileyJan 7 '14 at 17:42

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Nothing in modern science asserts that life arises by chance or accident. It arises from natural forces. You might has well say that rocks roll down hill, by "accident" and not gravity. Evolution is driven by energy from light and heat finding the maximal entropy path through organic molecules. The molecules accelerate entropy by forming complex structures dissipative structures. It's just like water turns from chaotic liquid into organized ice to shed heat or currents forming complex whirlpools to shed energy from friction of current against current. Nothing random at or chance at all.
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TechZenOct 4 '14 at 3:01

@TechZen - Interesting conjecture, but I'm not sure how it is meant to relate to the question or to my answer.
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Mark BaileyOct 6 '14 at 18:54

The problem is that most curricula on evolution already point out very clearly a large amount (although encompassing only a small fraction of the total) of experimental evidence, while creationism tries to justify its assertation by pointing out the few gaps of evidence within evolutionary biology. One must also remember that the Catholic Church itself does not reject evolution as "an attack on their sacred beliefs".
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March HoMar 11 at 6:47

@MarchHo The problem with this discussion is that too many people on both sides would rather dismiss other ways of thinking as invalid. The core of a Creationist view is not the fallacies they seek in the case for evolutionary biology, but the record of prophets. As you point out, there is not necessarily any contradiction between what is written in scripture and what science has discovered. But when you approach a person who is already certain of the truth of scripture, and begin to belittle what they know to be true, YOU CREATE opposition, and begin to convince them that evolution is a lie.
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Mark BaileyMar 12 at 15:52

...which leads to "the design inference", which posits that the characteristic of intelligence is able to overcome the problem established by the no-go: that life exist, but could not allegedly have arisen from a random process.

Now certain no-go theorems claim something is physically impossible, like transmitting information faster than the speed of light, some are about the provability in mathematics like Godel Incompleteness theorem, but the ID no-go theorem is about being statistically imprlausible- but what is implausible in a Big, Old Universe? Something like 1/Number of atoms in the universe is sufficiently low (2^82), and you can demonstrate this easily by thinking of DNA code 1/4^N where N = min num of base pairs for self-replication, where N~100,000 M genitalium. This is a very naive model, but it's a start: see George Chaitan's work for better maths: http://www.youtube.com/watch?v=RlYS_GiAnK8

The design inference is really Stephen Meyer's domain, and I'll refer you to him, this is much more a philosophic argument. One thing that's important to note for people who are dismissive of ID is that this is about reasoning about intelligence in the abstract, not the manifestation in physical form, not "some being".

What's my opinion? Could I get back to you in 300 years? We'll finally have data on thousands of other planets and whether any of them have ever harbored life, and that I think would be the falsification of ID if other life was found. But I think both a barren universe, and one with other life are both plausible given what we know now. That's why I don't get why people are so staunch on this issue: it's impossible to know the one key thing we need to know in this debate in our lifetime. But in a few generations we in fact will have this answer. We get to live in some interesting times.

Why would finding independent extraterrestrial life disprove ID? If we find ET, it might be vastly different, perhaps not even DNA or RNA based, or based on right-handed amino acids. Or perhaps we could discover something so hauntingly similar that we could almost have expected to find it here on Earth. In either case, I don't see that it offers any evidence against ID, or even against one single Intelligence. If I discover Mona Lisa and postulate that paintings must be created by humans, later discovering The Last Supper or The Persistence of Memory proves nothing to me either way.
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Mark BaileyDec 30 '13 at 21:01

If we find life arose independently somewhere else (or even twice on Earth), it would substantially change the range of probability that life could arise by random process. That's the first component I described, which can be answered thru data. I think it's the second component, the inference - which you have a problem with.
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user2437016Dec 31 '13 at 20:30

No. You're already presupposing that life arises by random process; ergo finding another instance of emergence proves that such random emergence is more likely than previously assumed. But this is circular logic. If instead, you presupposed that all life was created by Intelligence, finding another independent creation of life would lead you to conclude that this same Intelligence, or perhaps some entirely other Intelligence, has created this new world full of life. If you presuppose nothing, you know nothing new about the Go/No-Go probability, nor the inference.
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Mark BaileyDec 31 '13 at 21:04

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You can't calculate the probability of some pattern occurring without understanding mechanism that creates the pattern. Calculating the odds that molecules would form into certain patterns, without known the electron dynamics that force atom into specific configurations under specific conditions, would show that every clump of matter in the universe was fantastically improbable. But once you know the rules of chemistry, it looks deterministic,not improbable. The same applies to evolution. Once you understand the thermodynamics, improbability disappears.
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TechZenOct 4 '14 at 3:09